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(-) Description

Title :  HUMAN POLY(ADP-RIBOSE) POLYMERASE 10, CATALYTIC FRAGMENT IN COMPLEX WITH AN INHIBITOR 3-AMINOBENZAMIDE
 
Authors :  T. Karlberg, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Kotenyova, A. Kotzsch, T. K. Nielsen, P. Nordlund, T. Nyman, C. Persson, A. K. Roos, J. Sagemark, P. Schutz, M. I. Siponen, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Welin, M. Wisniewska, H. Schuler
Date :  26 May 09  (Deposition) - 16 Jun 09  (Release) - 16 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Parp, Poly(Adp-Ribose) Polymerase, Nad, Transferase, Structural Genomics, Structural Genomics Consortium, Sgc, Cytoplasm, Glycosyltransferase, Nucleus, Phosphoprotein, Polymorphism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Karlberg, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Kotenyova, A. Kotzsch, T. K. Nielsen, P. Nordlund, T. Nyman, C. Persson, A. K. Roos, J. Sagemark, P. Schutz, M. I. Siponen, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Welin, M. Wisniewska, H. Schuler
Human Poly(Adp-Ribose) Polymerase 10, Catalytic Fragment In Complex With An Inhibitor 3-Aminobenzamide
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLY [ADP-RIBOSE] POLYMERASE 10
    ChainsA, B
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-CH
    Expression System StrainBL21(DE3) R3 PRARE
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, UNP RESIDUES 809-1017
    GenePARP10
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPARP-10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
13AB2Ligand/Ion3-AMINOBENZAMIDE
2NA2Ligand/IonSODIUM ION
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:48 , ARG A:904 , LYS A:916 , ARG A:961 , ARG B:904 , ARG B:961BINDING SITE FOR RESIDUE PO4 A 1
2AC2SOFTWAREARG A:852 , ASN A:936 , ASP A:938 , HIS A:940BINDING SITE FOR RESIDUE PO4 A 2
3AC3SOFTWAREHOH A:26 , CYS A:876 , GLU A:877 , ARG A:878 , ASP A:952 , HOH B:78 , GLU B:877BINDING SITE FOR RESIDUE PO4 A 3
4AC4SOFTWAREHOH A:61 , HOH A:144 , GLY A:967 , HIS A:970 , LEU A:972BINDING SITE FOR RESIDUE NA A 5
5AC5SOFTWAREHIS A:887 , GLY A:888 , ALA A:911 , TYR A:919 , LEU A:926 , SER A:927 , TYR A:932BINDING SITE FOR RESIDUE 3AB A 1025
6AC6SOFTWAREHOH B:12 , HOH B:162 , GLY B:967 , HIS B:970 , LEU B:972BINDING SITE FOR RESIDUE NA B 4
7AC7SOFTWAREHIS B:887 , GLY B:888 , TYR B:919 , SER B:927 , TYR B:932BINDING SITE FOR RESIDUE 3AB B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HKV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:879 -Pro A:880
2Arg B:879 -Pro B:880

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HKV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HKV)

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7cENST000003130287cENSE00002167233chr8:145060622-14506052697PAR10_HUMAN1-110--
1.7kENST000003130287kENSE00001306487chr8:145060401-145060223179PAR10_HUMAN1-61610--
1.7vENST000003130287vENSE00001310975chr8:145060143-145059889255PAR10_HUMAN61-146860--
1.7aaENST000003130287aaENSE00001290625chr8:145059816-145059580237PAR10_HUMAN146-225800--
1.8cENST000003130288cENSE00001309960chr8:145059496-145058712785PAR10_HUMAN225-4862620--
1.9aENST000003130289aENSE00001250833chr8:145058599-145058378222PAR10_HUMAN487-560740--
1.9dENST000003130289dENSE00001250825chr8:145058272-14505817697PAR10_HUMAN561-593330--
1.9gENST000003130289gENSE00001250817chr8:145057979-145057335645PAR10_HUMAN593-8082160--
1.10ENST0000031302810ENSE00001250807chr8:145057233-145057100134PAR10_HUMAN808-852452A:817-852
B:818-852
36
35
1.11ENST0000031302811ENSE00001250800chr8:145052249-145052075175PAR10_HUMAN853-911592A:853-911
B:853-911
59
59
1.12cENST0000031302812cENSE00002140641chr8:145051998-145051328671PAR10_HUMAN911-10251152A:911-1008
B:911-1008
98
98

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:192
 aligned with PAR10_HUMAN | Q53GL7 from UniProtKB/Swiss-Prot  Length:1025

    Alignment length:192
                                   826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006  
         PAR10_HUMAN    817 WNNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFARRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHVP 1008
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhhh................eeee.hhhhhh...........eeeeeeeeee...eee.....................eee.......eeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:817-852           Exon 1.11  PDB: A:853-911 UniProt: 853-911                 ------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.12c  PDB: A:911-1008 UniProt: 911-1025 [INCOMPLETE]                                         Transcript 1 (2)
                3hkv A  817 WNNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFAKRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAMDCICQPSIFVIFHDTQALPTHLITCEHVP 1008
                                   826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006  

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with PAR10_HUMAN | Q53GL7 from UniProtKB/Swiss-Prot  Length:1025

    Alignment length:191
                                   827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007 
         PAR10_HUMAN    818 NNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFARRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAVDCICQPSIFVIFHDTQALPTHLITCEHVP 1008
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeee..hhhhhhhhhh................eeee.hhhhhh............eeeeeeee....eee.....................eee.......eeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.10  PDB: B:818-852          Exon 1.11  PDB: B:853-911 UniProt: 853-911                 ------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------Exon 1.12c  PDB: B:911-1008 UniProt: 911-1025 [INCOMPLETE]                                         Transcript 1 (2)
                3hkv B  818 NNLERLAENTGEFQEVVRAFYDTLDAARSSIRVVRVERVSHPLLQQQYELYRERLLQRCERRPVEQVLYHGTTAPAVPDICAHGFNRSFCGRNATVYGKGVYFAKRASLSVQDRYSPPNADGHKAVFVARVLTGDYGQGRRGLRAPPLRGPGHVLLRYDSAMDCICQPSIFVIFHDTQALPTHLITCEHVP 1008
                                   827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007 

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3HKV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HKV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HKV)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PAR10_HUMAN | Q53GL7)
molecular function
    GO:0070530    K63-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein.
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0048147    negative regulation of fibroblast proliferation    Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1900045    negative regulation of protein K63-linked ubiquitination    Any process that stops, prevents or reduces the frequency, rate or extent of protein K63-linked ubiquitination.
    GO:0033159    negative regulation of protein import into nucleus, translocation    Any process that stops, prevents or reduces the vectorial transfer of a protein from the cytoplasm into the nucleus, across the nuclear membrane.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    GO:0070213    protein auto-ADP-ribosylation    The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein.
    GO:0070212    protein poly-ADP-ribosylation    The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain.
    GO:0010847    regulation of chromatin assembly    Any process the modulates the frequency, rate or extent of chromatin assembly. Chromatin assembly is the assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        PAR10_HUMAN | Q53GL72dhx 5lx6

(-) Related Entries Specified in the PDB File

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